engine.cpp

   1 /*
   2  *  engine.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 8/15/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  *  There's a TON of duplicated code between InteractEngine and BatchEngine
   9  *  I couldn't figure out how to transition between ifstream (batch) and cin (interact)
  10  *  Fix later, don't have time now.
  11  *
  12  */
  13
  14
  15 #include "engine.hpp"
  16
  17 /***********************************************************************/
  18 Engine::Engine(){
  19         try {
  20                 cFactory = CommandFactory::getInstance();
  21                 mout = MothurOut::getInstance();
  22         }
  23         catch(exception& e) {
  24                 mout->errorOut(e, "Engine", "Engine");
  25                 exit(1);
  26         }
  27 }
  28 /***********************************************************************/
  29 string Engine::findMothursPath(){
  30         try {
  31
  32                 string envPath = getenv("PATH");
  33                 string mothurPath = "";
  34
  35                 //delimiting path char
  36                 char delim;
  37                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  38                         delim = ':';
  39                 #else
  40                         delim = ';';
  41                 #endif
  42
  43                 //break apart path variable by ':'
  44                 vector<string> dirs;
  45                 mout->splitAtChar(envPath, dirs, delim);
  46
  47                 //get path related to mothur
  48                 for (int i = 0; i < dirs.size(); i++) {
  49                         //to lower so we can find it
  50                         string tempLower = "";
  51                         for (int j = 0; j < dirs[i].length(); j++) {  tempLower += tolower(dirs[i][j]);  }
  52
  53                         //is this mothurs path?
  54                         if (tempLower.find("mothur") != -1) {  mothurPath = dirs[i]; break;  }
  55                 }
  56
  57                 if (mothurPath != "") {
  58                         //add mothur so it looks like what argv would look like
  59                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  60                                 mothurPath += "/mothur";
  61                         #else
  62                                 mothurPath += "\\mothur";
  63                         #endif
  64                 }else {
  65                         //okay mothur is not in the path, so the folder mothur is in must be in the path
  66                         //lets find out which one
  67
  68                         //get path related to mothur
  69                         for (int i = 0; i < dirs.size(); i++) {
  70
  71                                 //is this mothurs path?
  72                                 ifstream in;
  73                                 string tempIn = dirs[i];
  74                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  75                                         tempIn += "/mothur";
  76                                 #else
  77                                         tempIn += "\\mothur";
  78                                 #endif
  79                                 mout->openInputFile(tempIn, in, "");
  80
  81                                 //if this file exists
  82                                 if (in) { in.close(); mothurPath = tempIn;  break;  }
  83                         }
  84                 }
  85
  86                 return mothurPath;
  87
  88         }
  89         catch(exception& e) {
  90                 mout->errorOut(e, "Engine", "findMothursPath");
  91                 exit(1);
  92         }
  93 }
  94 /***********************************************************************/
  95
  96 InteractEngine::InteractEngine(string path){
  97
  98
  99         string temppath = path.substr(0, (path.find_last_of("othur")-5));
 100
 101         //this will happen if you set the path variable to contain mothur's exe location
 102         if (temppath == "") { path = findMothursPath(); }
 103
 104         mout->argv = path;
 105 }
 106
 107 /***********************************************************************/
 108
 109 InteractEngine::~InteractEngine(){}
 110
 111 /***********************************************************************/
 112 //This function allows the user to input commands one line at a time until they quit.
 113 //If the command is garbage it does nothing.
 114 bool InteractEngine::getInput(){
 115         try {
 116                 string input = "";
 117                 string commandName = "";
 118                 string options = "";
 119                 int quitCommandCalled = 0;
 120
 121                 while(quitCommandCalled != 1){
 122
 123                         #ifdef USE_MPI
 124                                 int pid, processors;
 125                                 MPI_Status status;
 126                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 127                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 128
 129                                 if (pid == 0) {
 130
 131                         #endif
 132
 133                         mout->mothurOutEndLine();
 134
 135                         input = getCommand();
 136                         mout->mothurOutEndLine();
 137
 138                         if (mout->control_pressed) { input = "quit()"; }
 139
 140                         //allow user to omit the () on the quit command
 141                         if (input == "quit") { input = "quit()"; }
 142
 143
 144                         #ifdef USE_MPI
 145                                 //send commandName
 146                                 for(int i = 1; i < processors; i++) {
 147                                                 int length = input.length();
 148                                                 MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 149                                                 MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 150
 151                                         }
 152                                 }else {
 153                                         int length;
 154                                         MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 155                                         //recieve container
 156                                         char* tempBuf = new char[length];
 157                                         MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 158
 159                                         input = tempBuf;
 160                                         if (input.length() > length) { input = input.substr(0, length);  }
 161                                         delete tempBuf;
 162                                 }
 163
 164
 165                         #endif
 166
 167                         CommandOptionParser parser(input);
 168                         commandName = parser.getCommandString();
 169
 170                         options = parser.getOptionString();
 171
 172                         if (commandName != "") {
 173                                         mout->executing = true;
 174                                         #ifdef USE_MPI
 175                                                 int pid;
 176                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 177
 178                                                 if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 179                                         //cout << pid << " is in execute " << commandName << endl;
 180                                         #endif
 181                                         //executes valid command
 182                                         mout->runParse = true;
 183                                         mout->Groups.clear();
 184                                         mout->namesOfGroups.clear();
 185                                         mout->Treenames.clear();
 186                                         mout->names.clear();
 187                                         mout->saveNextLabel = "";
 188
 189                                         Command* command = cFactory->getCommand(commandName, options);
 190                                         quitCommandCalled = command->execute();
 191
 192                                         //if we aborted command
 193                                         if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
 194
 195                                         mout->control_pressed = 0;
 196                                         mout->executing = false;
 197
 198                                         #ifdef USE_MPI
 199                                                 }
 200                                         #endif
 201                                 }else {
 202                                         mout->mothurOut("Invalid.");
 203                                         mout->mothurOutEndLine();
 204                                 }
 205                 }
 206                 return 1;
 207         }
 208         catch(exception& e) {
 209                 mout->errorOut(e, "InteractEngine", "getInput");
 210                 exit(1);
 211         }
 212 }
 213 /***********************************************************************/
 214 string Engine::getCommand()  {
 215         try {
 216
 217                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 218                         #ifdef USE_READLINE
 219                                 char* nextCommand = NULL;
 220                                 nextCommand = readline("mothur > ");
 221
 222                                 if(nextCommand != NULL) {  add_history(nextCommand);  }
 223                                 else{ //^D causes null string and we want it to quit mothur
 224                                         strcpy(nextCommand, "quit");
 225                                         mout->mothurOut(nextCommand);
 226                                 }
 227
 228                                 mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
 229                                 return nextCommand;
 230                         #else
 231                                 string nextCommand = "";
 232                                 mout->mothurOut("mothur > ");
 233                                 getline(cin, nextCommand);
 234                                 mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
 235
 236                                 return nextCommand;
 237                         #endif
 238                 #else
 239                                 string nextCommand = "";
 240
 241                                 mout->mothurOut("mothur > ");
 242                                 getline(cin, nextCommand);
 243                                 mout->mothurOutJustToLog(toString(nextCommand));
 244
 245                                 return nextCommand;
 246                 #endif
 247
 248
 249         }
 250         catch(exception& e) {
 251                 mout->errorOut(e, "Engine", "getCommand");
 252                 exit(1);
 253         }
 254 }
 255 /***********************************************************************/
 256 //This function opens the batchfile to be used by BatchEngine::getInput.
 257 BatchEngine::BatchEngine(string path, string batchFileName){
 258         try {
 259
 260                 openedBatch = mout->openInputFile(batchFileName, inputBatchFile);
 261
 262                 string temppath = path.substr(0, (path.find_last_of("othur")-5));
 263
 264                 //this will happen if you set the path variable to contain mothur's exe location
 265                 if (temppath == "") { path = findMothursPath(); }
 266
 267                 mout->argv = path;
 268
 269         }
 270         catch(exception& e) {
 271                 mout->errorOut(e, "BatchEngine", "BatchEngine");
 272                 exit(1);
 273         }
 274 }
 275
 276 /***********************************************************************/
 277
 278 BatchEngine::~BatchEngine(){    }
 279
 280 /***********************************************************************/
 281 //This Function allows the user to run a batchfile containing several commands on Dotur
 282 bool BatchEngine::getInput(){
 283         try {
 284                 //check if this is a valid batchfile
 285                 if (openedBatch == 1) {
 286                         mout->mothurOut("unable to open batchfile");
 287                         mout->mothurOutEndLine();
 288                         return 1;
 289                 }
 290
 291                 string input = "";
 292                 string commandName = "";
 293                 string options = "";
 294
 295                 //CommandFactory cFactory;
 296                 int quitCommandCalled = 0;
 297             int count = 0;
 298                 while(quitCommandCalled != 1){
 299
 300                         #ifdef USE_MPI
 301                                 int pid, processors;
 302                                 MPI_Status status;
 303                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 304                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 305
 306                                 if (pid == 0) {
 307
 308                         #endif
 309
 310                         input = getNextCommand(inputBatchFile);
 311                         count++;
 312
 313                         #ifdef USE_MPI
 314                                 //send commandName
 315                                 for(int i = 1; i < processors; i++) {
 316                                                 int length = input.length();
 317                                                 MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 318                                                 MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 319
 320                                         }
 321                                 }else {
 322                                         int length;
 323                                         MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 324                                         //recieve container
 325                                         char* tempBuf = new char[length];
 326                                         MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 327
 328                                         input = tempBuf;
 329                                         if (input.length() > length) { input = input.substr(0, length);  }
 330                                         delete tempBuf;
 331                                 }
 332
 333
 334                         #endif
 335
 336
 337
 338                         if (input[0] != '#') {
 339
 340                                 mout->mothurOutEndLine();
 341                                 mout->mothurOut("mothur > " + input);
 342                                 mout->mothurOutEndLine();
 343
 344                                 if (mout->control_pressed) { input = "quit()"; }
 345
 346                                 //allow user to omit the () on the quit command
 347                                 if (input == "quit") { input = "quit()"; }
 348
 349                                 CommandOptionParser parser(input);
 350                                 commandName = parser.getCommandString();
 351                                 options = parser.getOptionString();
 352
 353                                 if (commandName != "") {
 354                                         mout->executing = true;
 355                                         #ifdef USE_MPI
 356                                                 int pid;
 357                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 358
 359 //cout << pid << " is here " << commandName << '\t' << count << endl;
 360                                                 if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 361                                         #endif
 362                                         //executes valid command
 363                                         mout->runParse = true;
 364                                         mout->Groups.clear();
 365                                         mout->namesOfGroups.clear();
 366                                         mout->Treenames.clear();
 367                                         mout->names.clear();
 368                                         mout->saveNextLabel = "";
 369
 370                                         Command* command = cFactory->getCommand(commandName, options);
 371                                         quitCommandCalled = command->execute();
 372
 373                                         //if we aborted command
 374                                         if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
 375
 376                                         mout->control_pressed = 0;
 377                                         mout->executing = false;
 378
 379                                         #ifdef USE_MPI
 380                                                 }
 381                                         #endif
 382                                 }else {
 383                                         mout->mothurOut("Invalid.");
 384                                         mout->mothurOutEndLine();
 385                                 }
 386
 387                         }
 388                         mout->gobble(inputBatchFile);
 389                 }
 390
 391                 inputBatchFile.close();
 392                 return 1;
 393         }
 394         catch(exception& e) {
 395                 mout->errorOut(e, "BatchEngine", "getInput");
 396                 exit(1);
 397         }
 398 }
 399 /***********************************************************************/
 400 string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
 401         try {
 402
 403                 string nextcommand = "";
 404
 405                 if (inputBatchFile.eof()) { nextcommand = "quit()"; }
 406                 else { nextcommand = mout->getline(inputBatchFile); }
 407
 408                 return nextcommand;
 409         }
 410         catch(exception& e) {
 411                 mout->errorOut(e, "BatchEngine", "getNextCommand");
 412                 exit(1);
 413         }
 414 }
 415
 416 /***********************************************************************/
 417 /***********************************************************************/
 418 //This function opens the batchfile to be used by BatchEngine::getInput.
 419 ScriptEngine::ScriptEngine(string path, string commandString){
 420         try {
 421
 422                 //remove quotes
 423                 listOfCommands = commandString.substr(1, (commandString.length()-1));
 424
 425                 string temppath = path.substr(0, (path.find_last_of("othur")-5));
 426
 427                 //this will happen if you set the path variable to contain mothur's exe location
 428                 if (temppath == "") { path = findMothursPath(); }
 429
 430                 mout->argv = path;
 431
 432         }
 433         catch(exception& e) {
 434                 mout->errorOut(e, "ScriptEngine", "ScriptEngine");
 435                 exit(1);
 436         }
 437 }
 438
 439 /***********************************************************************/
 440
 441 ScriptEngine::~ScriptEngine(){  }
 442
 443 /***********************************************************************/
 444 //This Function allows the user to run a batchfile containing several commands on mothur
 445 bool ScriptEngine::getInput(){
 446         try {
 447
 448                 string input = "";
 449                 string commandName = "";
 450                 string options = "";
 451
 452
 453                 //CommandFactory cFactory;
 454                 int quitCommandCalled = 0;
 455
 456                 while(quitCommandCalled != 1){
 457
 458                         #ifdef USE_MPI
 459                                 int pid, processors;
 460                                 MPI_Status status;
 461                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 462                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 463
 464                                 if (pid == 0) {
 465
 466                         #endif
 467
 468                         input = getNextCommand(listOfCommands);
 469
 470                         if (input == "") { input = "quit()"; }
 471
 472                         if ((!mout->gui) || (input != "quit()")) {
 473                                 mout->mothurOutEndLine();
 474                                 mout->mothurOut("mothur > " + input);
 475                                 mout->mothurOutEndLine();
 476                         }
 477
 478                         #ifdef USE_MPI
 479                                 //send commandName
 480                                 for(int i = 1; i < processors; i++) {
 481                                                 int length = input.length();
 482                                                 MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 483                                                 MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 484
 485                                         }
 486                                 }else {
 487                                         int length;
 488                                         MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 489                                         //recieve container
 490                                         char* tempBuf = new char[length];
 491                                         MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 492
 493                                         input = tempBuf;
 494                                         if (input.length() > length) { input = input.substr(0, length);  }
 495                                         delete tempBuf;
 496                                 }
 497
 498
 499                         #endif
 500
 501
 502                         if (mout->control_pressed) { input = "quit()"; }
 503
 504                         //allow user to omit the () on the quit command
 505                         if (input == "quit") { input = "quit()"; }
 506
 507                         CommandOptionParser parser(input);
 508                         commandName = parser.getCommandString();
 509                         options = parser.getOptionString();
 510
 511                         if (commandName != "") {
 512                                         mout->executing = true;
 513                                         #ifdef USE_MPI
 514                                                 int pid, numProcesses;
 515
 516                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 517                                                 MPI_Comm_size(MPI_COMM_WORLD, &numProcesses);
 518
 519 //cout << pid << " is here " << commandName  << endl;
 520                                                 if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 521                                                         //cout << pid << " is in execute" << endl;
 522                                         #endif
 523                                         //executes valid command
 524                                         mout->runParse = true;
 525                                         mout->Groups.clear();
 526                                         mout->namesOfGroups.clear();
 527                                         mout->Treenames.clear();
 528                                         mout->names.clear();
 529                                         mout->saveNextLabel = "";
 530
 531                                         Command* command = cFactory->getCommand(commandName, options);
 532                                         quitCommandCalled = command->execute();
 533
 534                                         //if we aborted command
 535                                         if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
 536
 537                                         mout->control_pressed = 0;
 538                                         mout->executing = false;
 539
 540                                         #ifdef USE_MPI
 541                                         //cout << pid << " is done in execute" << endl;
 542                                                 }
 543                                         #endif
 544                                 }else {
 545                                         mout->mothurOut("Invalid.");
 546                                         mout->mothurOutEndLine();
 547                                 }
 548
 549
 550                 }
 551
 552                 return 1;
 553         }
 554         catch(exception& e) {
 555                 mout->errorOut(e, "ScriptEngine", "getInput");
 556                 exit(1);
 557         }
 558 }
 559 /***********************************************************************/
 560 string ScriptEngine::getNextCommand(string& commandString) {
 561         try {
 562
 563                 string nextcommand = "";
 564                 int count = 0;
 565                 bool ignoreSemiColons = false;
 566
 567                 //go through string until you reach ; or end
 568                 while (count < commandString.length()) {
 569
 570                          //you want to ignore any ; until you reach the next '
 571                         if ((commandString[count] == '\'') && (!ignoreSemiColons)) {  ignoreSemiColons = true;  }
 572                         else if ((commandString[count] == '\'') && (ignoreSemiColons)) {  ignoreSemiColons = false;  }
 573
 574                         if ((commandString[count] == ';') && (!ignoreSemiColons)) {  break;   }
 575                         else {          nextcommand += commandString[count];    }
 576
 577                         count++;
 578                 }
 579
 580                 //if you are not at the end
 581                 if (count != commandString.length())  {   commandString = commandString.substr(count+1, commandString.length());  }
 582                 else { commandString = ""; }
 583
 584
 585                 //get rid of spaces in between commands if any
 586                 if (commandString.length() > 0) {
 587                         while (commandString[0] == ' ') {
 588                                 commandString = commandString.substr(1,commandString.length());
 589                                 if (commandString.length() == 0) {  break;  }
 590                         }
 591                 }
 592
 593                 return nextcommand;
 594         }
 595         catch(exception& e) {
 596                 mout->errorOut(e, "ScriptEngine", "getNextCommand");
 597                 exit(1);
 598         }
 599 }
 600 /***********************************************************************/